Search found 19 matches

by jbhopkins
2021.01.22 18:59
Forum: ATSAS package in general
Topic: Problems with ATSAS 3.0.3 on Debian 10
Replies: 0
Views: 5

Problems with ATSAS 3.0.3 on Debian 10

Hi all, I'm struggling with ATSAS 3.0.3 on Debian 10 (buster, 10.6 is my exact version). I downloaded the .deb package and followed the install instructions. Upon running in the install I got this: ~/Downloads$ sudo dpkg --install ATSAS-3.0.3-1_amd64.deb Selecting previously unselected package atsas...
by jbhopkins
2021.01.04 17:09
Forum: ATSAS package in general
Topic: Issues with installation
Replies: 1
Views: 72

Re: Issues with installation

Hi, I'm the developer for RAW. It's not clear to me if this is a RAW issue or an ATSAS issue, but generally speaking for problems with RAW you'll want to post them to the RAW mailing list here: https://groups.google.com/g/bioxtas_raw Anyways, in order to help you troubleshoot, please let me know wha...
by jbhopkins
2020.10.14 17:23
Forum: Mixtures and flexible systems
Topic: Bug in EOM Rsigma calculation?
Replies: 6
Views: 1323

Re: Bug in EOM Rsigma calculation?

Hi Daniel,

Thanks for looking into it. The juneom.eom file seemed to be too large to attach here, so I sent you an email.

Jesse
by jbhopkins
2020.10.12 18:27
Forum: Mixtures and flexible systems
Topic: Bug in EOM Rsigma calculation?
Replies: 6
Views: 1323

Re: Bug in EOM Rsigma calculation?

I just wanted to ping this question. Does anyone have any thoughts? Or can anyone validate my calculation of Rsigma? Even if you haven't had time to track down the bug in EOM, it would be great to know if my calculation of Rsigma from the data is accurate, so I can use that in publications.
by jbhopkins
2020.05.18 21:34
Forum: Mixtures and flexible systems
Topic: Bug in EOM Rsigma calculation?
Replies: 6
Views: 1323

Re: Bug in EOM Rsigma calculation?

Turns out I can't attach more than 5 files to a post. Here's the rest of the EOM files. The python script is the 'eom_std_check.txt', which I can't attach as .py.
by jbhopkins
2020.05.18 21:32
Forum: Mixtures and flexible systems
Topic: Bug in EOM Rsigma calculation?
Replies: 6
Views: 1323

Bug in EOM Rsigma calculation?

Hi folks, I'm using EOM from ATSAS 3.0.1, and I think the Rsigma is being calculated incorrect. Either that or I don't understand how the Rsigma calculation is being done (quite possible). I've attached the results of an EOM run on some good quality data (.dat file also attached). Most of the result...
by jbhopkins
2020.04.24 22:52
Forum: ATSAS package in general
Topic: Missing manual for datmw?
Replies: 1
Views: 782

Missing manual for datmw?

Hi folks, There doesn't seem to be a manual for datmw. It would be nice to have one, both to help me remember it exists, and to easily see what options are available (plus, I'd like the information on how to cite it!). The datmw -h command from the command line actually prints a pretty good descript...
by jbhopkins
2020.01.08 18:38
Forum: Ab initio shape determination
Topic: Error running dammif with 'small' data
Replies: 1
Views: 849

Error running dammif with 'small' data

Hi folks, I'm using DAMMIF from ATSAS 3.0.0 on MacOS 10.14.6. When I try to run dammif on the attached GNOM .out file in fast mode, I get the following error: "error: initial shape dimensions too small, check units" This happens regardless of whether I run it in interactive mode or with command line...
by jbhopkins
2019.11.07 18:21
Forum: Model evaluation and manipulation
Topic: ATSAS 3.0 damaver error
Replies: 2
Views: 1578

ATSAS 3.0 damaver error

Hi folks, Congrats on the ATSAS 3.0 release! However, I've been trying to use it on Windows 10 and I can't get damaver to run. I've tried both from the command line and from Primus. If I install ATSAS 3.0 in the default directory (C:/Program Files (x86)/ATSAS 3.0.0) I get this error when I try to ru...
by jbhopkins
2019.04.30 18:37
Forum: Mixtures and flexible systems
Topic: Problem with EOM output pdbs
Replies: 2
Views: 5752

Re: Problem with EOM output pdbs

Al, Thanks for the reply. While you're opening bug reports, can you open one for the fact that the distribution outputs don't report the pool average correctly (it's always 0.00, see attached file for details)? For those with a similar problem, I've attached a python script that renumbers the residu...
by jbhopkins
2019.04.29 16:49
Forum: Mixtures and flexible systems
Topic: Problem with EOM output pdbs
Replies: 2
Views: 5752

Problem with EOM output pdbs

Hi folks, I'm running EOM on a heterodimer construct connected by a flexible linker. I'm using ATSAS 2.8.4 on MacOS (my local machine). The structure of both domains is known from MX, and was fixed in EOM. The linker and some N and C terminus regions were left flexible. The pool was generated via RA...
by jbhopkins
2017.09.07 15:48
Forum: SAXS & SANS Software
Topic: BioXTAS RAW - analysis of SAXS and SEC-SAXS data
Replies: 0
Views: 14246

BioXTAS RAW - analysis of SAXS and SEC-SAXS data

Hi all, I wanted to quickly promote the BioXTAS RAW software. Here's a little information about the software: BioXTAS RAW is a GUI based, free, open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS dat...
by jbhopkins
2017.02.01 23:15
Forum: Primary data processing
Topic: GNOM 5 doesn't recognize .cfg file
Replies: 4
Views: 8257

Re: GNOM 5 doesn't recognize .cfg file

Daniel, I'm sure it was announced, but I can't say that I pay close attention to all of the package announcements. I also have to admit that I didn't test it previously, as I tend to try to stick to release versions (I have enough trouble with bugs in my own software!). Anyways, I'm sure I can make ...
by jbhopkins
2017.02.01 22:37
Forum: Primary data processing
Topic: GNOM 5 doesn't recognize .cfg file
Replies: 4
Views: 8257

Re: GNOM 5 doesn't recognize .cfg file

Daniel, Thanks for the response. You're right in that this particular config file doesn't contain anything fancy (it's just lysozyme data), but I've often used the config file as an easy way to automate generation of P(r) functions, either for lots of files with the same settings (varying just Dmax,...
by jbhopkins
2017.02.01 18:28
Forum: Primary data processing
Topic: GNOM 5 doesn't recognize .cfg file
Replies: 4
Views: 8257

GNOM 5 doesn't recognize .cfg file

Hi, I recently upgraded to ATSAS 2.8.0 on Windows 7. I'm trying to run GNOM using the standard .cfg file approach (as described in the manual), but it doesn't seem to recognize it. I've put the cfg in the same folder as my data, but when I run gnom from the command line, it fails to recognize it and...